This is actually pretty cool. I tried to imitate one of the successful fits from qpAdm, and found something quite similar, using my results:

Target = 34% Yemen + 33% MA1 + 23% Yamnaya + 10% Dai @ D = 0.3681

Terrible fit, but quite similar to what one finds with qpAdm. In fact, the combined MA1+Yamnaya score is almost identical to what one qpAdm fit showed with regard to my total Yamnaya-related ancestry. Also, the qpAdm fit had me at 9% Dai, and this has me at 10%, so it's basically the same result.

Nevermind got it working, i'm a numpty and forgot to save it as a tab delimited file. xD

It's interesting how it much, much prefers having Corded Ware in addition to Bell Beaker rather than the two alone. It doesn't like just having Bell Beaker and it really doesn't like just having Corded Ware. Also seems to favour Esperstedt_MN over HungaryGamba_EN as well. Don't really know how it all works as such so perhaps this is meaningless waffle, but the lowest score i've managed to get so far 0.0064 which is either:

European=(33*0.08+5*0.31+11*0.02+100*0.59)=2.64+1.55+0.22+59=63.41, pretty close to Lithuanian average leveland so on across the rest of the components.

Seems like combining three almost pure populations of EEF, European and Central Asian would pretty much work best for West Eurasians, as the script would basically just set the levels of each to what the population average is in the K9 spreadsheet (even if they're not historically plausible contributors). Georgian is the closest "pure" Central Asian component population in the list, but I'd guess it has too much EEF to work well as a contributor sometimes though which is why Kalash is better in some ways in the Yamnaya mixes. Some other populations can work well when they're in the right places though, I guess.

Founder effect. 2 random R1 men(R1a-Z283, R1b-L11) who lived ~6,000YBP< represent almost 50% of west and northeast European paternal lineages. Most paternal lineages from that time period are extinct or very very rare. There are other clear founder effects from that time period within I1a-DF29 and I2a2a-M223. Also, as R1b-L11 moved in west Europe it kept having regional founder effects(R1b-L21, R1b-DF27, R1b-U152, R1b-U106).

You don't see the same trend at all with mtDNA. One ~5,000YBP maternal lineage in a region of Europe will probably represent at most a few percent of the maternal lineages.

Can someone run Tuscans, using Yamna, Esperstedt_MN, Hungary_HG, and Cyproit as ancestors?

I had earlier used the ANE K8 PCA to get all possible European(Yamna-MN or Stuttgart)+West Asian ancestral proportions. I picked a random North Italian, who with Spanish_MN got in every possibility 70%> European(~55-60% MN, ~13-17% Yamna)+~30% West Asian(always on the lower ANE side, Caucasus doesn't work).

Test=German and DutchAncestor1=Unetice or Urnfield.Ancestor2=Unetice or Urnfield.Ancestor3=Unetice or Urnfield.Ancestor4=Tuscan

NL4's ANE K8 results are in the spreadhseet.

We have signs of genetic continuation of a North sea-type pop in Germany during the Bronze age, and I think some modern Germans are still very North-sea-like and some admixed with a Near eastern-shifted pop, not just EEF-shifted like Tuscans(Romans?).

Alberto: Because Basque don't get any teal, they result in a mix that would only give them 1% ANE, which is too low.

Good point, the EuroHG cluster is probably the main representative of mediation of "ANE" into Basques in K9, but since WHG populations get 100% EuroHG (it fails to distinguish well between SHG, WHG and EHG ancestry and you get a basically SHG cluster), you get this strange result in this mixture algorithm seems to imply low levels of ANE when populations are combined and this inevitably includes a fair amount of the WHG populations. Probably most extreme for the Basque population.

Notice French especially don't fit as a mixture of a North Sea-type Bronze age pop(German Unetice, Bell Beaker) and Esperstedt_MN.

This is why I don't think Southern-shifted North Euros like: West Germans, French, and South Dutch, aren't southern shifted only because of excess EEF ancestry. There's probably East Mediterranean ancestry from Roman times. That's why I chose Tuscans as a southern source.

Romans, who else would it be? I know the Roman empire was international, but I'm sure in the military and government people from Rome itself and surrounding areas were the majority, at least in its early days.

Germans, Dutch, and French quite clearly have some East Mediterranean ancestry. The same is even more obvious for Spanish, but their European side is more EEF.

It's not "Roman ancestry". The early neolithic samples in Central-Europe already have plenty of East-Med (the LBK samples average around 30%, the Hungarian NE1 also. ). But there was also another wave of farmers, not just EEF, coming from the Caucasus that brought also east-med with them, besides of West-Asian (which EEF lacked). And it's not the Yamnaya cos they don't have East-Med.

If the high proportion of Unetice in Poles "The beginning of the formation of the modern East Central European gene pool", then does the the higher presence of Unetician c.f. CWC suggest that the formation of Central European gene pool was more completely formulated by the mid Bronze age rather than EN-EBA .?

I guess that 9% Turkish could be the extra NE you're referring to. But it works quite worse with other populations, like Armenians, Georgians, Lebanese,... So it seems that the bit of East Eurasian helps there too.

And this is just an oracle, so I don't take the results too literally. But all the results can be tested with qpAdm for example, or formal stats, and get a better understanding. It would be interesting, for example, to see if Unetice and Alberstedt have still high EHG affinity as Yamnaya and CW or if they have more WHG/SHG affinity.

Mixing populations from very different time periods, and including populations from more recent periods, produces the best fits, but isn't informative.

The most informative tests are those that include plausible ancient source populations which we know had little or no contact with each other before the admixture event that we're testing.

So yeah, if you get a low score with the "usual suspects" then you're onto something.

On the other hand, you can't really test for, say, Corded Ware and Unetice admixture in modern populations at the same time, because it's very likely that Unetice was in large part of Corded Ware origin.

I'm really thinking there's something to that East Eurasian in myself and others on here. Over and over, on the Ktests I'm running, I repeatedly get Turk/Ataic stuff in Western Europe. Whereas Siberian is basically left alone. It's as if IR1 types didn't make an impact, but nomads incorporated in Roman ranks did. It's a possibility and I will keep digging. I'd say set up a test involving the Yakut and French. See if that is better than Nganasan. Maybe the four used could be French South, WHG, Yamnaya, Yakut.

Thanks for those tests. Very interesting that they agree with the high Motala affinity showed in these other less scientific tests I was making.

@David

Sure, these are tests that can show some hints, no need to take them literally. They need to pass other tests and filters. But I'm not just using random combinations, anyway.

For example, the Motala guys seem not only to have been invited to the party, but they actually might have played important roles. From Yamnaya to CW and then to other LNBA it's mostly adding Motala-like admixture (and bits of MN). Whether from West Yamnaya or from the Baltic, or both.

@Chad

Yes, some bits of East Eurasian might be also at play. For French I got the best score when adding Turkish to the mix. And while this other result is quite random (probably meaningless), I found it curious enough to share. Best match by far for Basques:

And I agree. But what is believable is not the same as having a fixed preconception and discard whatever doesn't match it. Just a few years ago it was not believable that R1b could have come to WE in the Bronze Age, now it looks more than likely.

We just need to keep an open mind and look at possibilities that are plausible, especially when the data points in that direction.

I actually always try to go for the option that makes more sense with the data available and argument my reasoning the best I can.

If these stats which (repeatedly) suggest Motala like ancestry are true, then my initial impression of CWC as a largely autonomous european plain development, albeit with some steppe admixture, remains possible

The Motala isn't real. The program is compensating for him not having a Middle Neolithic pop. He doesn't have a WHG source, so Motala is the best fit. Trust me, when I make the Motalas a component, they're not really anywhere.

I don't have any K8 or K9 data for my grandparents and my father, so I made a K15 sheet. This should work nicely as well, the Eurogenes K15 really isn't a bad calculator.

My paternal grandmother is from the Low German speaking part of East Prussia, from the surrounds of modern-day Braniewo in Warmia, close to the Baltic sea. There is no ancient DNA of the local substrate population, the Old (Baltic) Prussians, but Lithuanians should work as a substitute, and I also use Poles, because undoubtedly there was some Polish admixture as well, recognizable in surnames. The more interesting question will be: Where did the medieval German settlers come from? The local dialect suggests a core area in northernmost Germany, from the mouth of the Weser into Holstein. But eastern Holstein was also colonial area, with Frisians, Westphalians and Dutch settlers being involved, besides the Holstens. Historical sources also suggest that some of the settlers in Warmia were from the Lower Rhine and from Holland.

The best approximation I could find for my grandmother uses the Hinxton Anglo-Saxons:

But still, the best are clearly the Hinxton Anglo-Saxons. Which may suggest that the population of northern Germany has changed from Anglo-Saxon-like to what it's like now. An alternative explanation may be that northernmost Germans are still Anglo-Saxon like and the north German sample is just from a larger area of northern Germany.

This would suggest an Old Prussian and Polish admixture of 31%, taken together. Also interesting, that's considerable, but not as high as some have suggested (some thought it was closer to 50%). On the other hand there certainly were local differences, with northeastern East Prussia near present-day Kaliningrad (former Königsberg) having much stronger Old Prussian ancestry.

The modeling showing minimal Corded Ware admixture across northern Europe is based on faulty methodology.

The only way it's possible to achieve these results is to use samples with lots of Corded Ware/Yamnaya admixture in the first place, like Alberstedt_LN, Unetice_EBA or Bell_Beaker_LN, and/or to mix and match with modern samples, which are more mixed and therefore produce better fits.

And even then the post-Neolithic shift in uniparental markers in Europe speaks for itself.

Come on guys, this is really sad to watch. It's already happened, so what's the point of all of this whining?

I read this as follows:The local Celts were somewhere inbetween the French and the Austrians. Hinxton2 represents the Germanic influence. And Italian Abruzzo is most likely ancient Roman input. Close to Basel there was the important Roman colony Augusta Raurica, also known as Colonia Augusta Rauricorum. And southern Swabia south of the Danube was also quite a firm part of the Roman empire, with the major city Augusta Vindelicorum nearby. This would suggest that the Roman influence on the whole was rather Abruzzo-like than Tuscan-like. I think this makes sense; the Tuscans are more light-pigmented than other central Italians, they are atypical.

I also tried to replace the Italian_Abruzzo with Ashkenazi, but it's a worse fit.

My father's paternal (phased) half is best approximated by quite a similar result:

50% Hinxton4 + 36% North_German + 14% Italian_Abruzzo @ D = 6.7756

My paternal grandfather's ancestry was from near Basel, Switzerland, from both sides of the Rhine, thus from southwesternmost Germany and from northwestern Switzerland near the Rhine. Hence it's no surprise that his result is similar to my maternal grandmother's result. He seems to be a little more Germanic and less Roman. What's puzzling is that the Celtic component is much better approximated with Hinxton4, the Celtic Briton, than with the French and Austrians. But this is in line with my father's FTDNA "MyOrigins" analysis, where he has lots of the Northwest European component and 0% of the central European component. In fact, my grandfather and his father indeed looked very Northwest European, the grandfather more the Atlantic Basque-like type, the great-grandfather more like an English gentleman.

Did you look at the D-Stats posted by Tobus? Did you see look at Haak's own figures? Or David's own D-Stats the other day about Lithuanians?

Why do you find it so strange that some Motala-like HG have contributed genes to modern Europeans? It's not only reasonable to think so, there is data suggesting it quite clearly, and we have ancient samples that existed in Sweden!

I also tried to determine what my maternal grandfather is like by analyzing my own phased maternal half. According to Eurogenes K15 oracle, my maternal grandmother is best approximated as 87% South_Dutch + 13% Ossetic. Therefore I selected these two populations to represent my grandmother's influence.

Using only three populations (by selecting an outgroup that yields 0%), my maternal half is this:

To some extent this is because of noise. My maternal half (according to K15) has 3.76% Sub-Saharan. But my entire DNA just scores 0.59% Sub-Saharan. According to the new K6 I'm 0.97% Sub-Saharan. This is close to a significant amount of 1%. So I don't think this North African-like input is nothing more than noise, but it may be inflated. Judging from IBD sharing with my maternal grandmother, I have about 24.6% from her and 25.4% from my grandfather. This means my maternal half cannot be 64% North Italian as the first approximation suggested. But adding the Algerian or Mozabite input I can get my grandmother's influence closer to 50% on my maternal half, which is closer to the truth. For what it's worth, my grandfather had some resemblance with the Algerian footballer Samir Nasri, when he was young:http://upload.wikimedia.org/wikipedia/commons/e/e1/Samir_Nasri_Euro_2012_v2.jpg

I also found the San Marinese footballer Manuel Battistini to have a strangely exotic look, like Near Eastern or North African admixed:http://img.uefa.com/imgml/TP/players/3/2016/324x324/250011890.jpg

Alberto, it's because all Europeans have EHG, but not enough to be closer to EHG than Motala. If you look at the PCA, Northern Europeans fall under Motala because of EHG. If it were Motala ancestry then we would cluster between Loschbour, with no one more ANE like than Motala. This isn't the case. Most of us have about as much EHG/ANE as Motala, so they can't be a primary source. My K runs have Norwegians as the highest in Motala, at 3%, which makes sense.

It's possible to replace Alberstedt_LN with Yamnaya, this results in an equally good fit. The problem is just that it's not possible that there was a Samara Yamnaya-like wave into Germany which left no genetic trace in Bronze Age Hungary, and no archeological trace in Poland.

Big change and big improvement. Is it cheating? Yes, probably adding a modern population is cheating. But we don't have an ancient sample for that population, and then again, giving Yamnaya as the only option for Caucasus-like admixture in Europe is cheating too. The truth might be somewhere in between.

Well, the problem is just that this oracle works only with steps of 25%. I think an alternative to trying millions of possibilities is to proceed strategically, i.e. to think first what might make sense considering history and archeology, and then to try systematically.

So, according to K8 I don't have any noteworthy North African ancestry. Just some slight Samaritan, Jewish or Lebanese Christian admixture, undoubtedly from my Italian grandfather.

But what strikes me most is the very strong influence from Bronze Age Hungary, about 80%! This is much more than I could have inherited from my Italian ancestors alone. As you might know, 50% of my ancestry is from southern Germany and the German speaking part of Switzerland. Add to this 25% of North Italian ancestry.

Very strong influence from Bronze Age Hungary in both southern Germany/Switzerland and Italy - isn't this a hint to the origin of the Italo-Celts?

Archeologically it makes sense, both Tumulus and Urnfield culture may have originated somewhere in the Carpathian Basin.

"I think an alternative to trying millions of possibilities is to proceed strategically, i.e. to think first what might make sense considering history and archeology"

I agree. Based on experiments like that...

It looks like there's a lot of native Neolithic blood in Iberia. My guess is the same is true for Italy) and the Balkans. And I think there's a way to confirm with 4mix and Oracle they have LN/BA ancestry. I'll post later with evidence.

Basque in particular maybe something like 70% Neolithic SW European, with no Near eastern or North African.

We can't assume all of Iberians Euro_MN beyond what's in LN/BA and West Asians/North Africans is from Iberia, but it's safe to say it comes from far western Europe.

Yes, I tried it a lot with Bell Beaker and Unetice, but with HungaryGamba_BA I get lower distances. Also, strangely, with K8 input I get Bell Beaker scores of 0 - 4%, Unetice seems to work much better.

Alberto,The biggest issue to begin with, is your use of Esperstedt. Esperstedt is only about 17-19% more WHG than Stuttgart, where Gok2 is 33% WHG. That is in a place with solidly verifiable Neolithic presence. Lithuanian is a gray area. We aren't sure what they looked like, but there is a decent chance that they were even more WHG than that. That would almost totally eliminate any need for Motala. It works with what you give it, plain and simple. Without the right reference, you will be misled into something that is most likely incorrect. That is where logic needs to play in heavily.

I'm about ready to nuke Murcia Spain. Based on the assumption they're Spain_MN+LN/BA+Middle East+maybe WHG I have gone through over 100 tests exhausting almost every Middle Eastern pop and every LN/BA. This is really frustrating.

The bests fits I can get so far are... Most other scores are 0.03(very bad fit).

My goal here was to find who gave Spanish_Murcia most of their ANE, LN/BA or Caucasus pops.

It's pretty clear LN/BA probably is, even though few fits worked well. This is because when Caucasus pops take its place Spanish_Murcia is fitted as Loschbour+West Asian. The are some rare exceptions though where Spain_MN takes the place of Loschbour to raise WHG.

With K8 I was not finding good fits for Spanish. Best ones were something like Spain_EN + HungaryGamba_BA + Bedouin. Then using HungaryGamba_IA things improved considerably, but I think it doesn't make a lot of sense to use that sample.

That was actually a rhetorical question, because, with all due respect, obviously not much.

I'll give you a brief outline; archeology and linguistics tell us that Balts are the direct descendants of the Fatyanovo-Balanovo people, who became the eastern Corded Ware or Battle-Axe people.

Now, unfortunately, we don't have any ancient genomes from the Battle-Axe Culture, but the German Corded Ware samples should be pretty close. So let's try them in your test instead of Yamnaya, which doesn't make much sense considering that we have something closer to Battle-Axe.

It's a great fit, so we can say that genetics backs up archeology and linguistics in this case.

But could the fit be even better with Battle-Axe samples? Yes, almost certainly, because check out what Haak et al. say about their Corded Ware samples.

"Corded Ware can be modeled as 29.1% Esperstedt, 9.4% Samara_HG, and 61.5% Yamnaya, which suggests that the population of eastern migrants had a slightly higher proportion of EHG ancestry in its makeup than the Yamnaya sample from Samara. Such a conclusion might also be drawn from the f4-statistic presented in SI7 (Table S7.6) that shows f4(Corded_Ware_LN, Yamnaya; Karelia, Chimp) = -0.00001 (Z=0.0). If Corded_Ware_LN was a simple mixture of a population related to our Yamnaya sample and of Neolithic Europeans, this statistic should be negative. However, if Corded_Ware_LN is descended from a population that has a higher proportion of EHG ancestry than the Yamnaya population, then the dilution of EHG ancestry due to European Neolithic admixture (which would cause the statistic to be negative), would be counterbalanced by its increase due to this higher EHG ancestry (which would cause it to be positive). It is quite possible that the variable mixtures of EHG and farmer populations existed in the European steppe, and our Yamnaya population represents only a point in a continuum of such mixtures."

"I'll give you a brief outline; archeology and linguistics tell us that Balts are the direct descendants of the Fatyanovo-Balanovo people, who became the eastern Corded Ware or Battle-Axe people."

With all due respect, Dave, there is no direct evidence for what you have stated. "Baltic ethnogenesis " occurred in the 13th century, AD!

But I know hat you're *trying* to say- the Gene Pool of Northern Europe was created by the Bronze Age; with more minot admixture and homogenization subsequently.

But the creation of a distinct Baltic ethnies falls in the Middle Ages, when the Slavicization and Christianization of Poland created the necessary socio-political conditions for Baltic Chiefs to see their fellow "Balts" beyond mere local competitors, but as fellow "us" versus a Polish, Rus or Swedish "them". It didn't have anything to do with when R1a1a arrived in the Baltic rim

Anyway, IJ split is almost certainly much earlier than 36 kya (Karmin says 45 kya, Y Full says 43 kya). And why would it be in Eastern Europe anyway? I mean it could be, but why not West Asia?"

IMO,there are not to many regions were the ancient gene pool could be derived and/or combine with the spread of Indo-European languages.Have a look at this video [17mins]some interesting ideas that you may agree or disagree with. The point about Finns/Hungarians is interesting. Since they also occupy regions within Baltic.

"The Finno-Ugric peoples are any of several peoples of Eurasia who speak languages of the Finno-Ugric group of the Uralic language family, such as the Khanty, Mansi, Hungarians, Maris, Mordvins, Sámi, Estonians, Karelians, Finns, Udmurts and Komis.[1]"

I don't know. For me the debate is open. I think that figures pointing to over 50% Yamnaya or up to 80% CW are overestimated. But other people who know more than I do think they're right. So what can I say?

I see contradictory data, but mostly pointing to lower Yamnaya/CW than those estimates. I guess we'll have to wait for more DNA to know with certainty.

I'm not really sure where the Normans came from, but it probably wasn't from Sweden

From what we know, most of them came from The British isles, not directly from Scandinavia, mainly from Danelaw and they probably were a mixture maybe with celtic wives like in Iceland.But what is sure, the place names in Normandy are more Anglo-Danish

Really, something like Motala plus Unetice (or other post-Corded populations of Germany) seems to work OK for Lithuanians via Haak's models. (Haak's f4 outgroup models have both upsides and downsides relative to this ADMIXTURE based modelling. The downside of ADMIXTURE based modelling is that it's only as good as your ADMIXTURE values are at explaining within and between population variation). I don't really see that that's necessarily that implausible?

You can also get there via combining a MN population with a *lot* of WHG admixture (simulated by the Gokhem+Loschbour combo in Chad/David's example) with a Yamnaya like population with a more *EHG* than the one we have (simulated by Yamnaya plus EHG and essentially what David is talking about by Eastern Corded Ware).

Neither's particularly more compelling at the moment, based on the raw outgroup statistics (and ADMIXTURE it seems). But at least at the moment we know we have populations like SHG around the Baltic (and straight up WHG like populations probably weren't), we know populations like Unetice exist. And possibly some of the populations we call Corded Ware might have been more Unetice like than like the Corded Ware samples we have.Of course, one convincing challenge to this, atm, would be that the derived EDAR variant may be a bit lower in Lithuanians than expected for a SHG mixed population.

Alberto and David: f4(Corded_Ware_LN, Yamnaya; Karelia, Chimp) = -0.00001 (Z=0.0)Interesting stat. Suggests CW has less "ENF" admixture (or Neolithic at any rate) than Samara Yamnaya, as if both CW is as related to Karelia as Yamnaya despite having inevitably less EHG and more WHG as a proportion of its non-"ENF" ancestry.

Think of it this way if that doesn't make sense at first blush; if CW had logically exactly the same amount of HG vs ENF ancestry as Yamnaya, and all Yamnaya's was EHG while a bit more of CW's was WHG, then Yamnaya should be closer to Karelia.... which it isn't.

Despite that the K8 shows Yamnaya should having around 7% less ENF than CW.

This could be assessed further via f4 comparisons involving various Near Eastern populations and Yamnaya.

With only four pops, it's impossible to get every bit of admixture. There is surely more than Corded Ware involved. We have several groups from the LN,EBA that will be involved, plus Iron Age and possibly Uralic input.

As for Motala, it's without any good reason to assume that Motala people were in Lithuania. It is probably a mix of WHG and EHG. I think that Ajv52 would be a better candidate. They show EHG stuff, where Motala does not. The only thing I can get with Motala is Native American like stuff. Whether that was a first mix, prior to EHG stuff moving in, I'm not sure. I think it's possible that folks that are similar to Native Americans could've moved in first, with mtDNA C, and such. EHG could've then gone into Siberia after them. The same thing happened when reindeer herders went from the steppes, into the far north.

Thanks for your insights They make perfect sense. Certainly ""Motala plus Unetice (or other post-Corded populations of Germany) seems to work OK for Lithuamoans" is more parasiminous than arguing that the ancestral Lithuanuans were some ultra -WHG group which mixed some yamnaya group which was even more EHG than the currently samples Yamnaya examples (-from the Samara mind you: which is fairly Eastern). .

Motalas don't look like a straight EHG mix. They're different. They get the Amerindian part, in the EHG hunters, but none of the other component, or whatever it is. Not even supervised runs make the Motala as part EHG. The hunters on Gotland do however show EHG. The way it looks right now, Motala contributed next to nothing in modern Europeans.

Chad Thanks for your explanation It makes sense I understand that you're saying that Motala shows some older, perhaps Palaeo north eurasian component, and not the (perhaps more novel) EHG propper. But what is this based on? Surely not the original K15 which shows them slightly west of a midpoint between Laschbour and Karelia.

Now my points, and I think Aberto's, is not that modern europeans have a large component of Motala- dervived ancestry, but Motala-like ancestry, ie from outside Scandinavia.

Yes, exactly. When we're saying Motala-like, it doesn't mean they are direct descendants of the Motala guys. We're talking more generally about a population that was quite WHG-like, but with some amount of ANE.

It would be strange that there was a line separating 100% WHG from EHG (60% WHG - 40% ANE). There must have been a gradient. The exact places and proportions we don't know, but from the Baltic to maybe the north Pontic seems possible.

That's about as good as my best fit for Spanish_Murcia. It probably isn't literal because what are the chances Spanish are a mixture of a native pop who was close to 60% WHG and a pop like Syrians?"

Yes, obviously not literal. It only shows the best end result, but not the genesis that took place to get there.

The South and East Mediterranean admixture in Spaniards makes it complicated to find good matches by this method. Probably Basques would be a better starting point, and then add some Mediterranean (but non-European) to it.

- Download- Unzip- Double click on Past3.exe icon- Tick the box "Row attributes" in the top left corner- Double click on one of the "black" panels to activate the colors drop down menu- Choose the colors you want from the drop down menu

"It would be strange that there was a line separating 100% WHG from EHG (60% WHG - 40% ANE). There must have been a gradient. The exact places and proportions we don't know, but from the Baltic to maybe the north Pontic seems possible."

That's A Bingo . If one had to guess- it's be modern Poland, perhaps along the Vistula to the Dniester.

What is your thought about the North Pontic steppe? The Dnieper is about half way between Samara and Hungary. But it probably had stronger ties with the eastern steppe than with the Hungarian plains. So should be find pure EHG, pure WHG or something in between?

The mtDNA C from the Neolithic sites on the Dnieper suggest that EHG was present there at that time, but if so, we don't know when it got there and how much further west it was able to expand before the Bronze Age. Probably not much.

None of the ancient Hungarian samples until BR1 carry any traces of ANE/EHG, and the steppe runs from southern Ukraine to the Hungarian Basin, so that speaks volumes IMO.

But you see, if EHG where in the Dnieper, that makes things complicated.

Whenever they got there, did they find a WHG population and mixed with them?

Or where they there since the LGM and expanded north and east from there? (but in this case they should be all over EE).

In any case, if they were there in the Neolithic, what about late CT? CT reaches the Dnieper and they had contact with the people there. And CT did have a big population that somehow dispersed. If this population had ANE already, where did they disperse? It doesn't seem they went west to Hungary, so maybe north? Or south?

CT was a massive Neolithic horizon in terms of population. I doubt that the Neolithic foragers on the Dnieper had much of an effect on it.

The reason EHG/ANE made such a big impact on Europe during the Bronze Age was because of a rapid population expansion from an area that initially had very low population densities, so that EHG foragers weren't swamped by farmers.

"CT was a massive Neolithic horizon in terms of population. I doubt that the Neolithic foragers on the Dnieper had much of an effect on it."

Yes, I can agree with that. But then you go on with:

"The reason EHG/ANE made such a big impact on Europe during the Bronze Age was because of a rapid population expansion from an area that initially had very low population densities"

Don't you see a basic contradiction there? With such low population densities they couldn't have much impact on a massive population like CT, but suddenly a rapid expansion made them have a big impact in half of the known world.

Physical anthropological data suggests that Balts are not simply the descendants of the local Battle Axe people (the local variant of the Corded Ware). The Battle Axe people were more massive and hunter-gatherer-like than the central European Corded people. And during the Bronze Age, that is: after the Corded Ware period, more gracile, smaller faced people entered the Baltic, probably from the south.

Of course you can doubt the value of such non-genetical data. But then again, why is there considerable EEF admixture in the Baltic? There were no Neolithic farming cultures in the Baltic prior to the Corded Ware. And if the origin of the Corded people was EHG + something from the Caucasus, then actually there should be no EEF admixture in the Baltic. If the story had ended with the Battle Axe culture and if there were no Bronze Age migrations of LNBA people from the south.

Excellent point. Your evidence from physical anthro matches that obvously seen in PCAs etc. Modern Balts are not simply Corded Ware people. There were ongoing admixtures in periods after the early Bronze Age. Thus, it is to be doubted the local Baltic EBA variant of CWC was actually "Baltic".

Davidski: Can you think of a way to compare the levels of Basal Eurasian admixture in Yamnaya and Corded Ware?

Really not sure. Only ideas I have are based on the outgroup relationship where Basal Eurasian is supposed to be the only thing decreasing affinity to Ust Ishim or ENA in the absence of recent ENA admixture.

Similar to the regression I did comparing ENF from K8 to D Test Yamnaya Ust Ishim Chimp based on the D stats you ran for me.

Of course, those run into problems if affinity to Ust Ishim or an ENA outgroup turns out to be affected by other factors than Basal Eurasian.

to get a basic idea. The group with more basal should have less affinity to the UI / ENA, so those stats would be negative if Corded Ware was further from UI / Papuan, or positive if Yamnaya is further from UI / Papuan.

Other ancient populations with D stats of the same form gave: Alberstedt LN -0.0015, Bell_Beaker 0.0017, BenzigerodeHeimburg_LN -0.0044, Karsdorf_LN 0.0062, Halberstadt_LBA 0.0037, Unetice_EBA 0. So again, Karsdorf was less Basal (closer to Ust Ishim), and I think that sample was your reference for what the real new population moving into Europe may have been like. Bell Beaker and Alberstedt are more or less no different to Yamnaya in their Basal-ness, I would say based on the Z score.

(Using Dai as a control replacing Ust Ishim in a stat of the same form, which should work no long as no ENA admixture, gave Alberstedt -0.0042, Bell Beaker -0.0004, BenzigerodeHeimburg_LN -0.0078, Corded_Ware_LN 0.0048, Karsdorf_LN 0.0051, Halberstadt_LBA -0.0038, Unetice -0.0005. Some differences, still the same general pattern with the Dai based stat usually being -0.002 less than the equivalent Ust Ishim stat.).

That's just a couple stats though, another thing which might make it stronger maybe, I think, simply by the use of the law of averages would be to

It's looks like Spanish_Murcia is 75% or more LN/BA+Spain_MN, and 25% or less something North African+West Asian. Considering they have 35% WHG you need 75% something ~5,000YBP European(I think LN/BA is apart of that).

I've been able to get very good fits for French and all Iberians using SouthWest Asians(sometimes also NW Africans), Spain_MN, and LN/BA in ANE K8. Looks like there is a lot of Neolithic survival in Iberia(Euro side is more EEF than LN/BA), especially in Basque who are probably something like 70%.

I haven't looked into Italy yet. SouthEast Europe looks complicated because of their high ANE.

For the rest of Europe.

North sea and NorthEast Euros look basically like LN/BA. Continental Germans(not all), Hungarians, CzechSlovakians, etc. look like a mix of something SouthEastern(Mid east or southeast Europe) and LN/BA.

I learned how to use "sink" and it's incredible. You plug in 14 ancestor pops, and the machine gives you every possible 4-way mixture using those 14 ancestors for test.txt. It gives you 100s of results in 10> minutes.

If you already know how to use 4-mix, it'll be easy to use sink with this link.

I didn't use Loschbour in this one, because it is unlikely people like him lived in Spain in the last 5,000 years. I think the results confirm significant LN/BA in Iberia and significant native Neolithic ancestry.

Other Spanish will probably score higher in Spain_MN and less in Middle Eastern.

A suggestion, when trying to model ancient Near Eastern in your prediction model, use a combination of the following 4: Samaritan/Lebanese Christian (closest to ancient Levantines) and Armenian/Georgian (closest to ancient Anatolia-South Caucasus). All the Neolithic action was taking place in these regions.

A little more on the Basal Eurasian affinities of LNBA populations, on a tangent. I was looking at the Haak K16 ADMIXTURE graph to see if there were any obvious patterns there in the components that might suggest anything.

I was kind of annoyed at how the blue European HG (Motala / Loschbour) component was on the stacked underneath the teal component (which I guess is we could call "Other Yamnaya ancestry" for now), making it harder to judge absolute amounts of blue component in the populations, so I flipped some of the parts of the bar graphs.

http://i.imgur.com/5ZlH9Xt.png

Kind of confirms visually why it would be hard to generate the LNBA populations in this K16 ADMIXTURE *just* from e.g. Esperstedt_MN and the Samara Yamnaya. The level of European blue is fairly identical in LNBA Germans and Samara Yamnaya, while being lower in MN Europeans, so introducing Yamnaya into MN Europeans to give them teal alone wouldn't work - as it would reduce the level of overall blue "European".

If you used Esperstedt_MN and Samara Yamnaya to model LNBA in Haak's admixture run, you'd need to "top up" the blue European via a HG contribution. At least on the basis of their K16 ADMIXTURE (Haak's outgroup modelling is a little different).

The mix that would work with minimal or no additional contribution for LNBA would only really be BR1 and BR2 (Hungary Bronze Age sample 1) and Yamnaya. Something like 66% Hungary Bronze Age plus 33% Yamnaya / Corded Ware would seem OK for Bell Beaker, then 50:50 Hungary Bronze Age and Yamnaya for other LNBA groups like Unetice, visually. But then we've no evidence that BR1 populations were widespread at all, at the moment.

Matt Yet again, interesting incites. Well, I wouldn't be surprised if the Carpathian basin was central to it all. In fact, if go so far as calling it the 'capital' of Bronze Age europe . It was the centre of metallurgy throughout the period, from where secondary subsidiaries fed into / out of- from the Nordic region, and Central Germany, to the Upper Dnieper

Hard to tell which ADMIXTURE analysis is the right one. As I said, using David's K8 data, Bell_Beaker_LN seems to be best approximated by 47% Corded_Ware_LN + 29% Alberstedt_LN + 19% Spain_MN + 5% La_Brana-1.

Though it doesn't really matter which MN and WHG populations are used. This approximation makes sense because at least some admixture from the local Corded People has to be expected. And Alberstedt_LN may be just a late local Corded derived group with some farmer admixture. MN with slight extra WHG may be from local farmers popping up again, or, what's more likely, from a west-> east movement of farmers. At least with this K8 data, the addition of HungaryGamba_BA to the mix doesn't result in better approximations, as far as I have tested.

As for Alberto's suggestion that Unetice might be a mix of Motala-like people with Georgian-like ones: The earliest Proto-Unetice is from Moravia and Lower Austria. The epicenter was in southeastern Moravia. That's both far from Scandinavia and from the Caucasus. And moreover it is close to where BR1 has lived, who had 0% West Asian-teal-Georgian-like admixture.

@ Simon, yeah sure, if you use another LNBA population and a WHG like La Brana then I imagine those can together add enough extra WHG to allow a Corded Ware plus Spain MN model to work.

It's just if you try to use Corded Ware plus Spain MN in a 2 way mix, without anyone else, for Beakers or other LNBA it seems that you'd have a bit of a problem getting a fit. The combined population wouldn't be able to get enough WHG (or EuroHG at any rate, remember these ADMIXTURE can't really distinguish HGs very well) while having not too much teal and the right amount of EEF.

If you broke down Corded Ware, Alberstedt and an 80:20 Spain_MN:La_Brana mix, all three would have about fairly close levels of the blue HG component from Haak (Corded a little more, the last 80:20 mix a little less).

HungaryGamba_BA and Corded Ware just looks like a relatively easy 2 way mix for most LNBA populations, like Beakers, certainly for the Haak admixture. Looks like the simplest 2 way pair. I don't doubt that combinations of other LNBA plus 3 other populations could get even closer proportions matches than that pair, particularly for how other ADMIXTURE vary from what was in Haak.

There were at least over 100 0.00 results, so I I'll have to look back for all the good fits for Tuscans.

All the fits seem to be telling the same story. Tuscans fit best as about 50% west Asian with significant ANE and maybe some WHG, and 50% something similar to Bronze age Hungarians.

So their non-West Asian-like side is about as Middle Neolithic as it is Bell Beaker or Unetice-like. So we could be looking at significant Neolithic survival in Italy, or massive replacement by immigrants similar to Bronze age Hungarians.

Cyriot having significant WHG and less ENF than Saudi makes Tuscan's Middle Eastern higher than Spain_Murcia.

Considering Tuscans score about 30% WHG they can fit as over 60% mainland 5,000YBP European. Otzei though had significantly less WHG than other Europeans from his time. So, Tuscans may have even more native Neolithic blood than what these fits give. Add to that we don't know exactly who lived in Italy 5,000 years ago, all we have are mainland proxies.

Krefter (or anyone else), can you please provide some more info on using the 'Sink' option? Should I be expecting all possible combinations of 4, for a given specific list of populations? I do not seem to get it right following your instructions.

Are you sure that by including 'Syrian' you get the best possible fit for you? I would be curious to see what happens if you replace Syrian with Lebanese_Christian and then with Cypriot. I suspect the the model will fit slightly better.

I'd rather use Unetice than Bell_Beaker in 4mix. There's alot of variation in Late Neolithic Germans, probably because the admixture event between Middle Neolithic farmers and immigrants from East Europe had just occurred.

"Looking at the range of values for individuals it appears that modern Europeans are very close to the the bronze age samples."

It's obvious now that Bell Beaker, Corded Ware Unetice, Urnfield, Tumulus, etc. were the predecessors of most modern European ethnic groups. One way or another modern Euro countries are Bell Beaker, etc. folk who've changed alot culturally.

Bell Beaker, Unetice, etc. genetic types and linguistic-type(IE) had been running around for 2,000 years by the time they were first recorded in writing, and were by that time were the Celts, Italics, Germans, etc.

I think the K8 approximations with just slight Near Eastern and stronger Cypriot-like admixture describe my ancestry better than the K9 approximations with strong North African admixture.

Because it's against common sense to think that any region of Italy has up to 50% North African admixture. Slavery and free migration in Roman times probably resulted in rather random mixture than in the strong presence of one particular ethnic group.

On the other hand admixture with a Cypriot-like element seems to be present throughout mainland Italy and Sicily, in varying proportions. This must be related with the strong presence of y-haplogroup J2.

Modern y-haplogroup frequencies backup my opinion: The Romagna is dominated by R1b, J2a, E-V13 and G2a. Haplogroups typical for the southern Levant and for Northern Africa amount to 6.1% in Rimini (4.1% E-M123 + 2% E-V65) and to 10.3% in Bologna (6.9% J1 + 3.4% E-M81).

I have a simple technical question which may be obvious to most, but still unclear to me. Is the 4mix test utilizing data at the admixture components (i.e. K8) level or within the levels?

In other words, if 2 hypothetical populations have exactly the same K8 admixture components, will they be giving exactly the same results if you include them alternatively in the model? Apparently, 2 populations that have identical K8 components may have different genetic diversity within these components. My understanding is the such genetic diversity is not captured by the 4mix analysis. Correct?

Since what is entered as the target's data is nothing but admixture components, the 4mix analysis cannot but work with this, and so logically targets and populations with exactly the same components will behave exactly the same and are thus interchangeable.

Thanks a lot for the clarification. I thought that this was the answer but I just wanted to confirm with people who have more experience in population genetics.

By the way, very interesting analysis you present above. Note that in order to 'explain' the Greeks better, you need to throw in an additional Caucasus-like component which is not included in the ancient genomes. A good proxy population for that is Georgians. Check below:

Yes, I've noticed before that in central Greece and towards the north there is a higher Caucasus : Near Eastern ratio than on Crete or the West Anatolian coast, presumably because the early Greeks had a higher Caucasus admixture from their IE roots.

Regarding my own ancestry, my K8 based approximations are not really credible either. I could only be 62% HungaryGamba_BA if southern Germans were 100% HungaryGamba_BA, i.e. with 0% Germanic admixture, which is hard to believe. It's more credible that I'm 72% Bell Beaker, like the K9 based analysis suggests. But then what about the considerable North African admixture that is also suggested by K9? Perhaps it's not really North African but from a hitherto unsampled early southeast European farming population that was more basal than any EEF population sampled so far. Perhaps this was associated with the E-V13 that's rather common in the Romagna.

Yamnaya is equally basal as Starcevo_EN, Spain_MN, and the Iceman, and only marginally less basal than Spain_EN and LBK_EN; significantly *more* basal than Germany_MN and Corded_Ware_LN. Yet in K8 Spain_MN comes out as 54% Near Eastern, Corded_Ware as 31% Near Eastern, and Yamnaya as only 24% Near Eastern.

Corded Ware is only marginally more basal than East Asians and European hunter-gatherers.

@ Capra, yeah, you're right. I missed those new stats with CW when David posted them up, looking at them now. How does Germany_MN end up with an excess of more of an excess of sharing with Ust Ishim than EHG / Motala for example, following the model where all ancient Eurasian HG except Basal Eurasian and ENA are all equally related to UI, and Germany_MN we know has a lot of farmer ancestry (and not just via the K8 but other ADMIXTURE)? Puzzling.

Still, comparing the D(Test, Corded Ware, UI, Chimp) stats to D(Test, Yamnaya, UI, Chimp) as I said I would, there is pretty much always this -0.007 offset where the Corded Ware stat is lower than the Yamnaya stat. Especially if you discard the samples with low SNP overlap in the 10s of thousands, and especially from 300,000 SNP overlap up set.

Also, Capra re: patterns, I didn't want to clutter up an already too complicated or long post any more, but there are some weird patterns in the D (Pop, Yamnaya; Ust Ishim Chimp) stats and when compared vs the D (Pop, Yamnaya; Dai Chimp) for ancient populations.

http://textuploader.com/fetc - copy into a text file and save as CSV to look at as a spreadsheet.

When you compare the D (Pop, Yamnaya; Ust Ishim Chimp) stats with the D (Pop, Yamnaya; Dai Chimp), then what you find is that the Ust Ishim stat is most positive relative to the Dai stat in Kostenki14 and the Early Neolithic and Middle Neolithic relative to EHG influenced populations. All the ancient populations other than EHG are a little less related to Dai than you would expect from their Ust Ishim based stat, compared to Yamnaya (or Yamnaya is a little more related to Dai compared to its Ust Ishim affinity).

The two D stats graphed - http://i.imgur.com/fwsGvOX.png

I don't know if these patterns are real, or are caused by some low SNP overlap issue once you get three ancient populations together to test, and that really squeezes the available overlap in some instances. Some of that could be potentially tested by using D (Ust Ishim Dai, Ancient Pop, Chimp), D (Ust Ishim, San, Ancient Pop, Chimp), D (Dai, San, Ancient Pop, Chimp) stats to reduce the number of overlapping ancient populations. Dai San could provide similar information on Basal Eurasian in the presumed absence of ENA / African admixture. Or maybe rerun the stat set with some modern populations rather than Yamnaya as a check. Might try that if / when I can get my Linux running again.

But on the other hand, re: SNP overlap, many of the populations like Germany_MN and Iceman actually seem to have pretty good 300,000+ SNP overlap. Above two D stat graph pruned for only those above 300,000 SNP - http://i.imgur.com/ss14fQP.png

So, using Ust' Ishim as our reference point for basalness, Yamnaya is about as basal as Spain_MN, Unetice, Bell Beaker, Norwegians, Basques, and Scottish. LBK_EN is about as basal as English, French, and Czechs. Most Southern Europeans are considerably more basal (but this includes African of course) than Neolithic farmers. (They had to get all that E and J Y-DNA from somewhere.)

Corded Ware comes up significantly less basal than Yamnaya.

I don't think this can be some kind of artifact of using ancient DNA, because it persists when you swap in modern populations, for instance Czechs and Basques.

First of all I have been trying to model Stuttgart as a mix between a Near Eastern ancestral population and a known HG individual (i.e. Loschbour, La-Brana, etc.). I found that the best model was the following:

Stuttgart = 22% Loschbour + 78% Samaritan @ D = 0.0697

Now in my mind this means that whenever I am trying to model a modern population using ancient genomes and I want to throw in a Near Eastern component, I should be using Samaritans for that. When I actually tried to do this, it was not always working as the ideal model. For example, when I try to model Greeks, as a mix between Near Eastern, EEF, Caucasus and an early European IE population like Corded Ware, I get:

I know that the differences are small, but why should Cypriot improve this model compared to Samaritan? Samaritan are definitely more 'pure' in terms of Near Eastern ancestry. What the Cypriots add is more WHG and more ANE, but the model already had lots of these from Corded Ware and Georgian, respectively.

I guess my overall question is should I be right sticking with 'Samaritan' when modeling Near Eastern ancestry or should I be checking what best fits each population/individual? I have seen people in the blog using all sorts of populations for modelling Near Eastern ancestry, like Bedouin, Druze, Syrians, Iraqi Jews, etc.

"First of all I have been trying to model Stuttgart as a mix between a Near Eastern ancestral population and a known HG individual (i.e. Loschbour, La-Brana, etc.). "

One of the components in ANE K8 is "Near Eastern". Davidski created what lots of Neolithic Near easterns were probably like. It's pretty much the same thing as EEF, minus like 27% WHG which came from West Asia and SouthEast Europe.

So, there's no reason to try to find Near eastern ancestry percentages in Early European farmers. Modern Near easterns have mixed with ANE-types, Africans, and South Asians since EEF's ancestors left over 8,000 years ago.

For WHG I added my own to my spreadsheet which scores 100% WHG, instead of using Loschbour, La Brana-1, etc. because all their scores have a little noise.

"I know that the differences are small, but why should Cypriot improve this model compared to Samaritan? Samaritan are definitely more 'pure' in terms of Near Eastern ancestry."

Whether Samartian is more pure Near Eastern or not doesn't matter. This is all about numbers. Whether the mixture fits history or not doesn't matter to the calculator.

Cypriot is more similar to Greeks than other Near Easterns are, so that could be why.

The genetic landscape of the Near East has probably changed significantly since the Neolithic, so it depends which period you're focusing on and which populations you're modeling.

Despite some WHG-related admixture, Stuttgart is probably still the best proxy for populations from Neolithic Anatolia and maybe even the northern Levant.

Georgians might be useful proxies for the Neolithic Transcaucasian population that mixed with Eastern European hunter-gatherers on the steppe to form the pastoralists of the Bronze Age who then invaded the rest of Europe.

However, keep in mind that southern Europe, especially southeastern Europe, has seen gene flow from the post-Neolithic and even post-Islamic expansion Near East, so using various modern Near Eastern groups to model the Near Eastern ancestry of, say, Sicilians and Greeks, might work best.

EEFs I think are suppose to have originated around Greece. Maybe WHGs weren't there in the Neolithic, so throughout the Neolithic Greeks would have stayed Stuttgart-like.

All of Greek's ANE couldn't be from people similar to modern West Asians, some is definitely from Yamnaya-types north of the Caucasus. Whether or not Yamnaya-type blood in Greece today is from people who brought Greek language to Greece is debatele.

It would make sense that a lot of Iron age Greek blood is still there(majority?) and that Iron age Greek blood is a mix of Yamnaya-types and others.